Orofacial clefts are one of the most common congenital disorders seen in children. They can occur as isolated cases of cleft palate (CPO), or cleft lip with or without cleft palate (CL/P), or in combination with other birth defects. Orofacial clefts can be surgically corrected at a young age; however, there can be lifelong medical issues and decreased quality of life as a result. The genes explaining a modest percentage of orofacial clefts have been identified; however, the majority of the cases are not molecularly defined. Orofacial clefts are also common naturally occurring birth defects seen in the domestic dog, Canis familiaris. Inheritance studies have demonstrated an autosomal recessive inheritance pattern in at least three different dog breeds. This proposal aims to identify genetic factors that predispose individuals to orofacial clefts using the dog as a model organism. The domestic dog provides a unique mammalian model system. Unlike other model organisms, dogs share our living environment and medical care and are susceptible to naturally occurring birth defects. A short gestational window (63 days), large litters of full siblings and ease of DNA sample collection make the dog a useful model system. Tools developed from the complete canine genome sequence allow efficient mapping of disease-causing genes using few affected individuals. The 7X sequence of the dog genome and the associated discovery of single nucleotide polymorphisms (SNPs) have provided the necessary tools for complete genome wide association studies. Due to the relatively large extent of linkage disequilibrium (LD) within individual dog breeds, many fewer SNPs and fewer DNA samples are needed compared to human studies in order to identify significant genetic associations when mapping within a single breed. We propose to identify the causative genes and mutations for four loci that cause orofacial clefting in the dog. In order to accomplish this, we will expand our current sample collection of DNA, phenotypic classification and environmental data from naturally occurring cleft dogs and their relatives. Genome wide association analysis will be performed using affected individuals, unaffected control siblings and unrelated controls within two breeds using a new 173K SNP genotyping array which is extremely high density based on breed LD. Fine structure mapping and resequencing will be used to define candidate mutations for four loci causing orofacial clefting in dogs which will be validated in large cohorts of dog DNA samples from phenotyped individuals from multiple breeds. Preliminary data demonstrates the feasibility of this approach and the utility of the dog as a model for orofacial clefts. Using only 16 affected samples from a single breed, two significantly associated regions were identified by GWAS and narrowed to critical intervals of 1 Mb and 2.4 Mb each. By comparing genotypes of family members, both regions were shown to be inherited as independent simple recessive traits. Both regions are also novel with respect to known genes involved with orofacial cleft formation in humans or rodents. Phenotypically, one region appears to cause cleft lip and palate while the other causes cleft palate only. The proposed work in the dog is expected to lead to the identification of genes and pathways that are candidates for orofacial clefting in humans. The validation of the dog as a model system for human birth defects will open new avenues for the studies of these defects. By defining the genetic basis for parallel naturally-occurring disorders, we expect that genes and pathways not previously implicated in these diseases will be identified.